Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1765 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0325867223 sf0325865241 3 25867223 1.04E-13 1.58E-10
vg0400345487 sf0400344487 4 345487 1.14E-13 2.84E-10
vg1011003709 sf1010932529 10 11003709 2.32E-11 1.88E-08
vg1011003657 sf1010932477 10 11003657 8.77E-11 1.86E-08
vg0628071771 sf0628070773 6 28071771 7.37E-10 6.27E-07
vg1121892713 sf1121426584 11 21892713 8.71E-10 4.85E-07
vg1017929024 sf1017857796 10 17929024 1.74E-09 3.80E-06
vg0608423416 sf0608422417 6 8423416 1.10E-07 4.59E-06
vg1020503245 sf1020431724 10 20503245 1.77E-07 4.16E-06
vg0400034660 sf0400033660 4 34660 2.13E-07 6.69E-07
vg0415028838 sf0415019552 4 15028838 3.13E-07 1.03E-06
vg1010999956 sf1010928776 10 10999956 7.24E-06 3.19E-08